[Biococoa-dev] BCPairwiseAlignment & BCScoreMatrix

Koen van der Drift kvddrift at earthlink.net
Fri Mar 11 18:18:35 EST 2005

On Mar 11, 2005, at 4:31 PM, Alexander Griekspoor wrote:

> So Koen, in this light your remark:
>> I am thinking how this will be used. The end user probably wants to 
>> try out one type of alignment, see the result, then try another one, 
>> compare the results, etc. So if we make a BCNeedlemanWunsch, and then 
>> a BCSmithWaterman where is the actual matrix that is used to 
>> calculate. I think it is a good idea if we have just one matrix, that 
>> is used as a basis for each different calculation. It would be a 
>> waste if for every calculation the starting matrix has to be 
>> re-calculated. Or maybe that's where BCMatrix comes in place?
> The actual matrix used for calculation is the second one. But keeping 
> the matrix only saves you the memory allocation, but different 
> alignments fill the matrix differently so there's no use in keeping it 
> around as it has to be refilled again with scores based on algorithm, 
> penalty scores, gap costs etc. As most time goes into filling the 
> matrix and tracing it back after the fill, you can't reuse it. Also, 
> most algorithms that are subquadratic for memory requirements, chop up 
> the matrix and use a divide-and-conquer approach because it's the 
> storage of a complete-sized matrix that forms the memory problem.
> Does this make any sense?

Yes :)

- Koen.

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